Soybean cyst nematode (SCN;
Soybean growers widely use the
- NSF-PAR ID:
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Plant Direct
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Soybean cyst nematode (SCN;
Heterodera glycines) is the largest pathogenic cause of soybean yield loss. The Rhg1locus is the most used and best characterized SCN resistance locus, and contains three genes including one encoding an α‐SNAP protein. Although the Rhg1α‐SNAP is known to play an important role in vesicle trafficking and SCN resistance, the protein’s binding partners and the molecular mechanisms underpinning SCN resistance remain unclear. In this report, we show that the Rhg1α‐SNAP strongly interacts with two syntaxins of the t‐SNARE family (Glyma.12G194800 and Glyma.16G154200) in yeast and plants; importantly, the genes encoding these syntaxins co‐localize with SCN resistance quantitative trait loci. Fluorescent visualization revealed that the α‐SNAP and the two interacting syntaxins localize to the plasma membrane and perinuclear space in both tobacco epidermal and soybean root cells. The two syntaxins and their two homeologs were mutated, individually and in combination, using the CRISPR‐Cas9 system in the SCN‐resistant Peking and SCN‐susceptible Essex soybean lines. Peking roots with deletions introduced into syntaxin genes exhibited significantly reduced resistance to SCN, confirming that t‐SNAREs are critical to resisting SCN infection. The results presented here uncover a key step in the molecular mechanism of SCN resistance, and will be invaluable to soybean breeders aiming to develop highly SCN‐resistant soybean varieties.
We report reference‐quality genome assemblies and annotations for two accessions of soybean (
Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. maxassemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. sojaassemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single‐nucleotide polymorphisms ( snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snpdistributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan‐gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40–42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. sojaand the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.
Relative to homozygous diploids, the presence of multiple homologs or homeologs in polyploids affords greater tolerance to mutations that can impact genome evolution. In this study, we describe sequence and structural variation in the genomes of six accessions of cultivated potato (
Solanum tuberosumL.) ,a vegetatively propagated autotetraploid and their impact on the transcriptome. Sequence diversity was high with a mean single nucleotide polymorphisms ( SNP) rate of approximately 1 per 50 bases suggestive of high levels of allelic diversity. Additive gene expression was observed in leaves (3605 genes) and tubers (6156 genes) that contrasted the preferential allele expression of between 2180 and 3502 and 3367 and 5270 genes in the leaf and tuber transcriptome, respectively. Preferential allele expression was significantly associated with evolutionarily conserved genes suggesting selection of specific alleles of genes responsible for biological processes common to angiosperms during the breeding selection process. Copy number variation was rampant with between 16 098 and 18 921 genes in each cultivar exhibiting duplication or deletion. Copy number variable genes tended to be evolutionarily recent, lowly expressed, and enriched in genes that show increased expression in response to biotic and abiotic stress treatments suggestive of a role in adaptation. Gene copy number impacts on gene expression were detected with 528 genes having correlations between copy number and gene expression. Collectively, these data suggest that in addition to allelic variation of coding sequence, the heterogenous nature of the tetraploid potato genome contributes to a highly dynamic transcriptome impacted by allele preferential and copy number‐dependent expression effects.
CO2responses ( A/ Cicurves) are used to assess environmental responses of photosynthetic traits and to predict future vegetative carbon uptake through modeling. The recent development of rapid A/ Cicurves ( RACiRs) permits faster assessment of these traits by continuously changing [ CO2] around the leaf, and may reveal additional photosynthetic properties beyond what is practical or possible with steady‐state methods.
Gas exchange necessarily incorporates photosynthesis and (photo)respiration. Each process was expected to respond on different timescales due to differences in metabolite compartmentation, biochemistry and diffusive pathways. We hypothesized that metabolic lags in photorespiration relative to photosynthesis/respiration and
CO2diffusional limitations can be detected by varying the rate of change in [ CO2] during RACiR assays. We tested these hypotheses through modeling and experiments at ambient and 2% oxygen.
Our data show that photorespiratory delays cause offsets in predicted
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RACiRs may prove useful in assessing diffusional limitations to gas exchange and photorespiratory rates.
Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (
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